chr7-11514469-A-G

Variant names:

• chr7-11514469-A-G
• rs6972615
• NM_015204.3:c.1822+26950T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015204.3(THSD7A):​c.1822+26950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,070 control chromosomes in the GnomAD database, including 3,568 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.21 (3568 hom., cov: 32)
• Consequence: THSD7A NM_015204.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657
• Publications: 3 publications found

Genes affected

THSD7A (HGNC:22207): (thrombospondin type 1 domain containing 7A) The protein encoded by this gene is found almost exclusively in endothelial cells from placenta and umbilical cord. The encoded protein appears to interact with alpha(V)beta(3) integrin and paxillin to inhibit endothelial cell migration and tube formation. This protein may be involved in cytoskeletal organization. Variations in this gene may be associated with low bone mineral density in osteoporosis. [provided by RefSeq, Aug 2010]

ENSG00000230333 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015204.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	NM_015204.3	MANE Select	c.1822+26950T>C		intron	N/A	NP_056019.1	Q9UPZ6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	THSD7A	ENST00000423059.9	TSL:5 MANE Select	c.1822+26950T>C		intron	N/A	ENSP00000406482.2	Q9UPZ6
	ENSG00000230333	ENST00000445839.5	TSL:4	n.442-5583A>G		intron	N/A
	THSD7A	ENST00000497575.1	TSL:5	n.311+26950T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32542 AN: 151954 Hom.: 3562 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.224

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.214 AC: 32560 AN: 152070 Hom.: 3568 Cov.: 32 AF XY: 0.212 AC XY: 15762 AN XY: 74316

African (AFR) AF: 0.196 AC: 8137 AN: 41488

American (AMR) AF: 0.222 AC: 3390 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 902 AN: 3468

East Asian (EAS) AF: 0.214 AC: 1105 AN: 5174

South Asian (SAS) AF: 0.175 AC: 846 AN: 4824

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10558

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15196 AN: 67962

Other (OTH) AF: 0.226 AC: 478 AN: 2116

Alfa AF: 0.225 Hom.: 6568

Bravo AF: 0.214

Asia WGS AF: 0.195 AC: 679 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.40
PhyloP100		-0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6972615; hg19: chr7-11554096;